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- PDB-8zmz: Cryo-EM structure of R-eLACCO2 in the lactate-bound state -

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Basic information

Entry
Database: PDB / ID: 8zmz
TitleCryo-EM structure of R-eLACCO2 in the lactate-bound state
ComponentsLactate-binding periplasmic protein TTHA0766,Red fluorescent protein drFP583
KeywordsFLUORESCENT PROTEIN
Function / homology
Function and homology information


lactate transport / tripartite ATP-independent periplasmic transporter complex / bioluminescence / generation of precursor metabolites and energy / transmembrane transport / periplasmic space / calcium ion binding / protein homodimerization activity / zinc ion binding
Similarity search - Function
Lactate-binding periplasmic protein TTHA0766 / Solute binding protein, TakP-like / TRAP transporter solute receptor DctP / TRAP transporter solute receptor DctP superfamily / Bacterial extracellular solute-binding protein, family 7 / Green fluorescent protein, GFP / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein
Similarity search - Domain/homology
(2S)-2-HYDROXYPROPANOIC ACID / Lactate-binding periplasmic protein TTHA0766 / Red fluorescent protein drFP583
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
Discosoma sp. (sea anemone)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsKamijo, Y. / Kusakizako, T. / Nureki, O. / Campbell, R.E. / Nasu, Y.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
Japan Science and Technology Japan
CitationJournal: To Be Published
Title: Cryo-EM structure of ReLACCO2 in the lactate-bound state
Authors: Kamijo, Y. / Kusakizako, T. / Nureki, O. / Campbell, R.E. / Nasu, Y.
History
DepositionMay 24, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lactate-binding periplasmic protein TTHA0766,Red fluorescent protein drFP583
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,1753
Polymers70,0451
Non-polymers1302
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))

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Components

#1: Protein Lactate-binding periplasmic protein TTHA0766,Red fluorescent protein drFP583 / ABC transporter / solute-binding protein / Extracytoplasmic solute receptor protein TTHA0766 / TRAP ...ABC transporter / solute-binding protein / Extracytoplasmic solute receptor protein TTHA0766 / TRAP transporter lactate-binding subunit P / DsRed


Mass: 70044.500 Da / Num. of mol.: 1 / Mutation: mutant type
Source method: isolated from a genetically manipulated source
Details: Chimeric protein of THA0766 and cpmApple
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria), (gene. exp.) Discosoma sp. (sea anemone)
Gene: TTHA0766 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SK82, UniProt: Q9U6Y8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-2OP / (2S)-2-HYDROXYPROPANOIC ACID


Mass: 90.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H6O3 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: R-eLACCO2 in the lactate-bound state / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Thermus thermophilus H8 (bacteria)300852
21Discosoma sp. (sea anemone)86600
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 146454 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
ELECTRON MICROSCOPYs_bond_nonh_d0.0086342988945500.0116956264
ELECTRON MICROSCOPYs_angle_nonh_d1.5636123461521.64060631

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